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lines changed Original file line number Diff line number Diff line change @@ -64,6 +64,13 @@ too slow.
6464#### ` ped_file `
6565Family structures and sex assignments determined in [ EvidenceQC] ( ./eqc ) . See [ PED file format] ( /docs/gs/inputs#ped-format ) .
6666
67+ #### <HighlightOptionalArg >Optional</HighlightOptionalArg > ` outlier_sample_ids `
68+ Provide a file containing sample IDs, delimited by new lines, to exclude from the generation of batch metrics -
69+ this should can be based on outlier samples identified during sample QC that are still retained in the cohort. If
70+ provided, the workflow discards any outlier samples from being considered as part of the called samples when
71+ calculating metrics at a given site, as long as non-outlier samples are also called for that site. It does the
72+ same for the set of background samples considered in the metric calculations for a given site.
73+
6774## Outputs
6875
6976#### ` metrics `
Original file line number Diff line number Diff line change @@ -71,6 +71,11 @@ Per-sample binned read counts (`*.rd.txt.gz`) generated in the [GatherSampleEvid
7171Provide one of these inputs to subset the input batch. ` n_samples_subsample ` will randomly subset, while
7272` sample_ids_training_subset ` is for defining a predetermined subset. These options are provided for convenience in Terra.
7373
74+ #### <HighlightOptionalArg >Optional</HighlightOptionalArg > ` outlier_sample_ids `
75+ Provide a file containing sample IDs, delimited by new lines, to exclude from the from the gCNV model training
76+ process - this should can be based on outlier samples identified during sample QC that are still retained in the
77+ cohort.
78+
7479## Outputs
7580
7681#### ` cohort_contig_ploidy_model_tar `
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